/**
* Query SPARQL endpoint with a SELECT query
*
* @param qExec QueryExecution encapsulating the query
* @return model retrieved by querying the endpoint
*/
private Model getSelectModel(QueryExecution qExec) {
Model model = ModelFactory.createDefaultModel();
Graph graph = model.getGraph();
ResultSet results = qExec.execSelect();
while (results.hasNext()) {
QuerySolution sol = results.next();
String subject;
String predicate;
RDFNode object;
try {
subject = sol.getResource("s").toString();
predicate = sol.getResource("p").toString();
object = sol.get("o");
} catch (NoSuchElementException e) {
logger.error("SELECT query does not return a (?s ?p ?o) Triple");
continue;
}
Node objNode;
if (object.isLiteral()) {
Literal obj = object.asLiteral();
objNode = NodeFactory.createLiteral(obj.getString(), obj.getDatatype());
} else {
objNode = NodeFactory.createLiteral(object.toString());
}
graph.add(
new Triple(NodeFactory.createURI(subject), NodeFactory.createURI(predicate), objNode));
}
return model;
}
/**
* Perform the {@link QueryExecution} once.
*
* @param action
* @param queryExecution
* @param query
* @param queryStringLog Informational string created from the initial query.
* @return
*/
protected SPARQLResult executeQuery(
HttpAction action, QueryExecution queryExecution, Query query, String queryStringLog) {
setAnyTimeouts(queryExecution, action);
if (query.isSelectType()) {
ResultSet rs = queryExecution.execSelect();
// Force some query execution now.
// If the timeout-first-row goes off, the output stream has not
// been started so the HTTP error code is sent.
rs.hasNext();
// If we wanted perfect query time cancellation, we could consume
// the result now to see if the timeout-end-of-query goes off.
// rs = ResultSetFactory.copyResults(rs) ;
// action.log.info(format("[%d] exec/select", action.id)) ;
return new SPARQLResult(rs);
}
if (query.isConstructType()) {
Dataset dataset = queryExecution.execConstructDataset();
// action.log.info(format("[%d] exec/construct", action.id));
return new SPARQLResult(dataset);
}
if (query.isDescribeType()) {
Model model = queryExecution.execDescribe();
// action.log.info(format("[%d] exec/describe", action.id)) ;
return new SPARQLResult(model);
}
if (query.isAskType()) {
boolean b = queryExecution.execAsk();
// action.log.info(format("[%d] exec/ask", action.id)) ;
return new SPARQLResult(b);
}
ServletOps.errorBadRequest("Unknown query type - " + queryStringLog);
return null;
}
/**
* Returns the string value of the first of the properties in the uriDescriptionList for the given
* resource (as an URI). In case the resource does not have any of the properties mentioned, its
* URI is returned. The value is obtained by querying the endpoint and the endpoint is queried
* repeatedly until it gives a response (value or the lack of it)
*
* <p>It is highly recommended that the list contains properties like labels or titles, with test
* values.
*
* @param uri - the URI for which a label is required
* @return a String value, either a label for the parameter or its value if no label is obtained
* from the endpoint
*/
private String getLabelForUri(String uri) {
String result;
if (uriLabelCache.containsKey(uri)) {
return uriLabelCache.get(uri);
}
for (String prop : uriDescriptionList) {
String innerQuery = "SELECT ?r WHERE {<" + uri + "> <" + prop + "> ?r } LIMIT 1";
try {
Query query = QueryFactory.create(innerQuery);
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
boolean keepTrying = true;
while (keepTrying) {
keepTrying = false;
try {
ResultSet results = qExec.execSelect();
if (results.hasNext()) {
QuerySolution sol = results.nextSolution();
result = EEASettings.parseForJson(sol.getLiteral("r").getLexicalForm());
if (!result.isEmpty()) {
uriLabelCache.put(uri, result);
return result;
}
}
} catch (Exception e) {
keepTrying = true;
logger.warn("Could not get label for uri {}. Retrying.", uri);
} finally {
qExec.close();
}
}
} catch (QueryParseException qpe) {
logger.error("Exception for query {}. The label cannot be obtained", innerQuery);
}
}
return uri;
}
/**
* Get a set of unique queryObjName returned from a select query
*
* <p>Used to retrieve sets of modified objects used in sync
*
* @param rdfQuery query to execute
* @param queryObjName name of the object returned
* @return set of values for queryObjectName in the rdfQuery result
*/
HashSet<String> executeSyncQuery(String rdfQuery, String queryObjName) {
HashSet<String> rdfUrls = new HashSet<String>();
Query query;
try {
query = QueryFactory.create(rdfQuery);
} catch (QueryParseException qpe) {
logger.warn(
"Could not parse [{}]. Please provide a relevant query. {}",
rdfQuery,
qpe.getLocalizedMessage());
return null;
}
QueryExecution qExec = QueryExecutionFactory.sparqlService(rdfEndpoint, query);
try {
ResultSet results = qExec.execSelect();
while (results.hasNext()) {
QuerySolution sol = results.nextSolution();
try {
String value = sol.getResource(queryObjName).toString();
rdfUrls.add(value);
} catch (NoSuchElementException e) {
logger.error("Encountered a NoSuchElementException: " + e.getLocalizedMessage());
return null;
}
}
} catch (Exception e) {
logger.error(
"Encountered a [{}] while querying the endpoint for sync", e.getLocalizedMessage());
return null;
} finally {
qExec.close();
}
return rdfUrls;
}
/**
* A method to build a collection of collaborator objects representing a network based on an
* organisation
*
* @param id the id of the central organisation
* @param radius the number of edges required from the central contributor
* @return the collection of collaborator objects
*/
@SuppressWarnings("rawtypes")
public TreeMap<Integer, Collaborator> getRawCollaboratorData_org(String id, int radius) {
// check the parameters
if (InputUtils.isValidInt(id) == false) {
throw new IllegalArgumentException("Error: the id parameter is required");
}
if (InputUtils.isValidInt(radius, ExportServlet.MIN_DEGREES, ExportServlet.MAX_DEGREES)
== false) {
throw new IllegalArgumentException(
"Error: the radius parameter must be between "
+ ExportServlet.MIN_DEGREES
+ " and "
+ ExportServlet.MAX_DEGREES);
}
// define helper variables
// collection of collaborators
java.util.TreeMap<Integer, Collaborator> cId_cObj_map =
new java.util.TreeMap<Integer, Collaborator>();
// set of collaborators that we've already processed
java.util.TreeSet<Integer> foundCollaboratorsSet = new java.util.TreeSet<Integer>();
// define other helper variables
String contributor_id = null;
QuerySolution row = null;
Collaborator collaborator = null;
String sql =
"SELECT DISTINCT b.eventid "
+ "FROM events a, orgevlink b "
+ "WHERE b.organisationid = ? " // +id
+ "AND a.eventid = b.eventid";
int[] param = {Integer.parseInt(id)};
java.sql.ResultSet resultSet = db.exePreparedStatement(sql, param);
ArrayList<String> eventResults = new ArrayList<String>();
try {
// check to see that data was returned
if (!resultSet.last()) {
db.tidyup();
return null;
} else resultSet.beforeFirst();
// loop through the resultset
while (resultSet.next() == true) {
eventResults.add(resultSet.getString(1));
}
} catch (java.sql.SQLException ex) {
System.out.println("Exception: " + ex.getMessage());
resultSet = null;
}
db.tidyup();
// helper
int first = 0;
// define the query
String sparqlQuery1 =
"PREFIX foaf: <"
+ FOAF.NS
+ "> "
+ "PREFIX ausestage: <"
+ AuseStage.NS
+ "> "
+ "PREFIX event: <http://purl.org/NET/c4dm/event.owl#> "
+ "PREFIX dcterms: <http://purl.org/dc/terms/> "
+ "SELECT DISTINCT ?agent ?givenName ?familyName "
+ "WHERE { ";
for (String event : eventResults) {
if (first > 0) {
sparqlQuery1 += "UNION ";
}
first++;
sparqlQuery1 +=
"{<ausstage:e:"
+ event
+ "> a event:Event; "
+ " event:agent ?agent. "
+ " ?agent a foaf:Person; "
+ " foaf:givenName ?givenName; "
+ " foaf:familyName ?familyName. "
+ " } ";
}
sparqlQuery1 += " } ";
// execute query
ResultSet results = rdf.executeSparqlQuery(sparqlQuery1);
// now we transfer the results to a TreeMap <Integer,
while (results.hasNext()) {
row = results.nextSolution();
contributor_id = AusStageURI.getId(row.get("agent").toString());
collaborator = new Collaborator(contributor_id);
cId_cObj_map.put(Integer.parseInt(contributor_id), collaborator);
foundCollaboratorsSet.add(Integer.parseInt(contributor_id));
}
rdf.tidyUp();
return cId_cObj_map;
} // end getRawCollaboratorData_org method
/*
* add some of the additional required information for collaborator
*/
public ArrayList<Collaborator> getCollaborators(
TreeMap<Integer, Collaborator> network, String id) {
// declare helper variables
java.util.ArrayList<Collaborator> collaborators = new java.util.ArrayList<Collaborator>();
// define a SPARQL query to get details about a collaborator
String sparqlQuery =
"PREFIX foaf: <"
+ FOAF.NS
+ ">"
+ "PREFIX ausestage: <"
+ AuseStage.NS
+ "> "
+ "SELECT ?collabName ?function ?gender ?nationality "
+ "WHERE { "
+ " @ a foaf:Person ; "
+ " foaf:name ?collabName. "
+ "OPTIONAL {@ ausestage:function ?function} "
+ "OPTIONAL {@ foaf:gender ?gender} "
+ "OPTIONAL {@ ausestage:nationality ?nationality} "
+ "} ";
String queryToExecute = null;
ResultSet results = null;
QuerySolution row = null;
Collaborator collaborator = null;
// loop through the list of collaborators and get additional information
Collection networkKeys = network.keySet();
Iterator networkKeyIterator = networkKeys.iterator();
Integer networkKey = null;
Integer centreId = Integer.parseInt(id);
// loop through the list of keys
while (networkKeyIterator.hasNext()) {
// get the key for this collaborator
networkKey = (Integer) networkKeyIterator.next();
// create a new collaborator object
collaborator = new Collaborator(networkKey.toString());
// build the query
queryToExecute =
sparqlQuery.replaceAll(
"@", "<" + AusStageURI.getContributorURI(collaborator.getId()) + ">");
// execute the query
results = rdf.executeSparqlQuery(queryToExecute);
// add details to this contributor
while (results.hasNext()) {
// loop though the resulset
// get a new row of data
row = results.nextSolution();
// add the data to the collaborator
collaborator.setName(row.get("collabName").toString());
if (row.get("function") != null) {
collaborator.setFunction(row.get("function").toString());
}
if (row.get("gender") != null) {
collaborator.setGender(row.get("gender").toString());
}
if (row.get("nationality") != null) {
collaborator.setNationality(row.get("nationality").toString());
}
collaborator.setUrl(AusStageURI.getContributorURL(collaborator.getId()));
}
// play nice and tidy
rdf.tidyUp();
results = null;
// add the collaborator to the list
collaborators.add(collaborator);
}
return collaborators;
}